This makes sense, however the people who have been bitten all seem to have been Windows users and we are accustomed to using tools such as Active State's ppm to install modules. We don't see the tar ball at all and, as far as I can see, there is no Doxyfile to copy. I suspect that many people who use cpan from a *nix command prompt may have the same issue because, again, there is no visible tar ball and no direct interaction with the unpacking process.

A better place for a template Doxyfile would be in the site/lib/Doxygen/Filter/Perl folder alongside the POD.pm file or perhaps in the parent folder alongside the Perl.pm file. In any case the current documentation doesn't make it at all clear where the template file should be, nor how a default Doxyfile should be altered to enable the Perl filter.